Diatoms are one of the most important eukaryotic primary producers in the lower ecosystem; understanding their evolutionary history is therefore also important. Throughout most of the Cenozoic hydrosphere, diatoms have flourished. However, as a result of progressive diagenesis and dissolution of the opaline silica that forms their frustules, their early evolution during the Cretaceous is unclear, so the fossil record is incomplete. Largely because of this poor fossil record, little is known about the mid-Cretaceous interval (Cenomanian to Turonian). This study presents a new fossil record of Cenomanian opaline diatoms in carbonate concretions hosting ammonites from Hokkaido in the northwestern Pacific Ocean. Primitive floral assemblages composed of dominantly cylindrical or discoid forms are associated with a few hemiaulid diatoms, one of the predominant taxa since the Campanian age. The Cenomanian diatoms are similar to late Early Cretaceous (Albian) flora reported mainly from the Southern Hemisphere, but given their association with a few taxa typical of the Late Cretaceous, they are somewhat transitional.